buffer overflow error about rascaf HOT 4 CLOSED

Can you please show me the command line you use? Can you see anything output to the result file specified from -o option (default output file is rascaf.out).

I'll create and upload a sample data set later.

Thanks.

from rascaf.

The command I'm using is the same as in the sample,

rascaf -b A.bam -f assembly.fa -o A

The A.out file begins as follows:

Contigs
0: scaffold10000_size206 1 206
1: scaffold10001_size206 1 206
2: scaffold10002_size206 1 206
3: scaffold10003_size206 1 206
4: scaffold10004_size206 1 206
5: scaffold10005_size206 1 206
6: scaffold10006_size206 1 206
7: scaffold10007_size206 1 206
8: scaffold10008_size206 1 206
9: scaffold10009_size206 1 206
10: scaffold1000_size26079 1 124
...

And continues until the end which is:

116307 scaffold_j128_1 99476 (18240 19653): (116308 scaffold_j128_1 99477 (19704 21040)):(1 2)
116308 scaffold_j128_1 99477 (19704 21040): (116307 scaffold_j128_1 99476 (18240 19653)):(2 2)
116309 scaffold_j128_1 99477 (21097 21124):
116310 scaffold_j128_1 99477 (21205 22036):
116311 scaffold_j128_1 99477 (22342 22499):
116312 scaffold_j128_1 99477 (22635 26001):
command line: /home/peter/bioinformatics/Rascaf/rascaf -b

from rascaf.

It seems the error happens when it trying to resolve the path to the alignment file. I've uploaded a more robust version. Can you give it a try?

From the output, are you also using the verbose mode?

Thanks

from rascaf.

The new version completed without error! The previous error was generated with the verbose mode flag included. Thanks for your help.

from rascaf.